Browse > Article
http://dx.doi.org/10.14480/JM.2016.14.4.174

Characterization of simple sequence repeats in the Pleurotus ostreatus cultivars, 'Heuktari' and 'Miso'  

Park, Bokyung (Gyeongsangnam-do Agricultural Research and Extension Services)
Ha, Byeong Seok (Gyeongsangnam-do Agricultural Research and Extension Services)
Kim, Min Keun (Gyeongsangnam-do Agricultural Research and Extension Services)
Lee, Byungjoo (Chungcheongnam-do Agricultural Research & Extension Services)
Choi, Jong In (Mushroom Research Institute, GARES)
Ryu, Jae-San (Gyeongsangnam-do Agricultural Research and Extension Services)
Publication Information
Journal of Mushroom / v.14, no.4, 2016 , pp. 174-178 More about this Journal
Abstract
Simple sequence repeats (SSR), also referred to "microsatellites" consist of tandemly repeated short DNA sequence motifs and have been applied in various marker-based studies. SSRs were isolated and characterized from 'Heuktari' and 'Miso', which are major oyster mushroom cultivars in Korea, by genome sequencing and bioinformatic analysis. The genome sizes of 'Heuktari' and 'Miso' were estimated to be 40.8 and 40.3 Mb, respectively, which are larger than those of other P. ostreatus species (PC9 and PC10) and smaller than those of P. eryngii (KNR2312P5). In total, 949 and 968 SSRs were found in the 'Heuktari' and 'Miso' genomes, respectively. Comparative analysis of five mushrooms including P. ostreatus var. florida (PC9 and PC15) and P. eryngii revealed that the number of SSRs in 'Heuktari' and 'Miso' were the highest among them. All mushrooms studied showed similar SSR distribution patterns. Tri-, hexa-, and octanucleotide motifs accounted for the top three fractions of all SSRs.
Keywords
Simple sequence repeat; Pleurotus ostreatus; Mushroom; Molecular marker;
Citations & Related Records
Times Cited By KSCI : 2  (Citation Analysis)
연도 인용수 순위
1 Carneiro MO, Russ C, Ross MG, Gabriel SB, Nusbaum C, DePristo MA. 2012. Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics 13:375.   DOI
2 Chistiakov DA, Hellemans B, Haley CS, Law AS, Tsigenopoulos CS., Kotoulas G, Bertotto D, Libertini A, Volckaert FA. 2005. A microsatellite linkage map of the European sea bass Dicentrarchus labrax L. Genetics. 170: 821-1826.
3 Choi JI, Lee YH, Ha TM, Jeon DH, Chi JH, Shin PG. 2015. Characteristics of new mid-high temperature adaptable oyster mushroom variety "Heuktari" for bottle culture. Journal of Mushroom. 13: 74-78.   DOI
4 Collard BCY, Mackill DJ. 2008. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences 363: 557-572.   DOI
5 da Maia LC, Palmieri DA, de Souza VQ, Kopp MM, de Carvalho FIF, Costa de Oliveira A. 2008. SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation. International Journal of Plant Genomics 2008:1-9.
6 Ellegren H. 2004. Microsatellites: simple sequences with complex evolution. Nat Rev Genet. 5: 435-445.
7 El-Rodeny W, Kimura M, Hirakawa H, Sabah A, Shirasawa K et al. 2014. Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba). Breeding Science. 64: 252-263.   DOI
8 Im CH, Park Y-H, Hammel KE, Park B, Kwon SW et al. 2016. Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii. Fungal Genetics and Biology. 92: 50-64.   DOI
9 Karaoglu H, Lee CMY, Meyer W. 2004. Survey of simple sequence repeats in completed fungal genomes. Molecular Biology and Evolution. 22: 639-649.   DOI
10 Labbe J, Murat C, Morin E, Le Tacon F, Martin F. 2011. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers. Current Genetics 57: 75-88.   DOI
11 Miah G, Rafii M, Ismail M, Puteh A, Rahim H et al. 2013. A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance. Inter J Molecular Sci. 14: 22499-22528.   DOI
12 Lee BJ, Kim YG, Kim HK, Yang ES, Lim YP. 2010. Studies on the development of mushroom media for bottle culture in new Pleurotus ostreatus 'Miso'. J Mushroom Sci Prod. 8: 37-40.
13 Li Y-C, Korol AB, Fahima T, Nevo E. 2004. Microsatellites Within Genes: Structure, Function, and Evolution. Mol Biol Evol. 21(6): 991-1007   DOI
14 Loire E, Higuet D, Netter P, Achaz G. 2013. Evolution of coding microsatellites in primate genomes. Genome Biol Evol. 5: 283-295.   DOI
15 Ministry for Agriculture, Food, Rural Affairs (MAFRA). Republic of Korea. 2016. The actual putout of oil seeds and cash crops in 2015:pp63
16 Moxon R, Bayliss C, Hood D. 2006. Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptation. Annu Rev Genet. 40: 307-333.   DOI
17 Qu J, Huang C, Zhang J. 2016. Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus. Gene. 575: 524-530.   DOI
18 Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D et al. 2014. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Pro Nat Acad Sci. 111: 9923-9928.   DOI
19 Ryu JS, Kim KH, Im CH, Je HJ, Kim MK, Chae SM. 2012. Complete Genome Sequence of Pleurotus eryngii KNR2312 Using the Next Generation Sequencing (NGS). 80th meeting of the mycological society of America. The mycological society of America. New Haven, CT. USA.
20 Wei W, Davis RE, Suo X, Zhao Y. 2015. Occurrence, distribution and possible functional roles of simple sequence repeats in phytoplasma genomes. Inter J syste evol microbiol. 65: 2748-2760.   DOI
21 Yoon M-Y, Moe KT, Kim D-Y, Rho I-R, Kim S et al. 2012. Genetic diversity and population structure analysis of strawberry (Fragaria x ananassa Duch.) using SSR markers.
22 Zhang P, Li J, Li X, Liu X, Zhao X, Lu Y. 2011. Population Structure and Genetic Diversity in a Rice Core Collection (Oryza sativa L.) Investigated with SSR Markers. PLoS One. 6: e27565.   DOI
23 Bindler G, Plieske J, Bakaher N, Gunduz I, Ivanov N et al. 2011. A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development. Theoretical and Applied Genetics. 123: 219-230.   DOI
24 Varshney RK, Bertioli DJ, Moretzsohn MC, Vadez V, Krishnamurthy L et al. 2009. The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.). Theo Appl Genetics. 118: 729-739.   DOI
25 Au KF, Underwood JG, Lee L, Wong WH. 2012. Improving PacBio long read accuracy by short read alignment. PLoS One. 7: e46679.   DOI
26 Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic acids research. 27: 573.   DOI